Many herbal products are now used as remedies to treat various infectious and non-infectious conditions. Even though the use of herbs and natural products is much more evident in the Eastern world, their use in Western cultures is continuously increasing. Although the immunomodulatory effects of some herbs have been extensively studied, research related to possible immunomodulatory effects of many herbs and various spices is relatively scarce. Here, we provide a comprehensive review of the immunomodulatory and anti-inflammatory properties of Nigella sativa, also known as black seed or black cumin, and its major active ingredient, thymoquinone (TQ). This review article focuses on analyzing in vitro and in vivo experimental findings that were reported with regard to the ability of N. sativa and TQ to modulate inflammation, cellular and humoral adaptive immune responses, and Th1/Th2 paradigm. The reported capability of N. sativa to augment the cytotoxic activity of natural killer (NK) cells against cancer cells is also emphasized. The molecular and cellular mechanisms underlying such immunomodulatory and anti-inflammatory effects of N. sativa and TQ are highlighted. Moreover, the signal transduction pathways implicated in the immunoregulatory functions of N. sativa and TQ are underscored. Experimental evidence suggests that N. sativa extracts and TQ can potentially be employed in the development of effective therapeutic agents towards the regulation of immune reactions implicated in various infectious and non-infectious conditions including different types of allergy, autoimmunity, and cancer.